Hermes Agent is an AI assistant that learns from its use by creating and improving skills, retaining knowledge, searching past conversations, and adapting to its users. It is for people who want to run an agent through a terminal or messaging platforms while connecting it to different AI models and scheduled tasks.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add NousResearch/hermes-agent --skill bioinformaticsgit clone --depth 1 https://github.com/NousResearch/hermes-agentWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/nousresearch/hermes-agent/bioinformatics)<a href="https://agentmods.dev/skills/nousresearch/hermes-agent/bioinformatics"><img src="https://agentmods.dev/badge/skills/nousresearch/hermes-agent/bioinformatics/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/nousresearch/hermes-agent/bioinformatics"><img src="https://agentmods.dev/badge/skills/nousresearch/hermes-agent/bioinformatics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Snyk warn
- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Privilege Escalation · line 221 Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.Fix: Avoid sudo/root unless strictly required. Prefer least-privilege patterns. If elevation is needed, document the justification and scope.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00015 | $0.03388 |
| Opus 5.5 | $0.00006 | $0.01355 |
| Sonnet 5.5 | $0.00003 | $0.00678 |
| Haiku 4.5 | $0.00002 | $0.00339 |
Grade B, and why
bioinformatics scanned grade B with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Asks for rootmediumPrivilege escalation
A mod that escalates privileges can change anything on the machine, not only the project.
sudo apt install samtools bcftools ncbi-blast+ minimap2 bedtools Copies of this mod
8 near-identical copies found in the catalogue:
- bioinformatics — 100% identical, 8 lines differ
- bioinformatics — 100% identical, 8 lines differ
- bioinformatics — 98% identical, 10 lines differ
- bioinformatics — 94% identical, 12 lines differ
- bioinformatics — 94% identical, 12 lines differ
- bioinformatics — 94% identical, 0 lines differ
- bioinformatics — 94% identical, 12 lines differ
- bioinformatics — 94% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 238 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Bioinformatics Skills Gateway
Use when asked about bioinformatics, genomics, sequencing, variant calling, gene expression, single-cell analysis, protein structure, pharmacogenomics, metagenomics, phylogenetics, or any computational biology task.
This skill is a gateway to two open-source bioinformatics skill libraries. Instead of bundling hundreds of domain-specific skills, it indexes them and fetches what you need on demand.
Sources
◆ bioSkills — 385 reference skills (code patterns, parameter guides, decision trees) Repo: https://github.com/GPTomics/bioSkills Format: SKILL.md per topic with code examples. Python/R/CLI.
◆ ClawBio — 33 runnable pipeline skills (executable scripts, reproducibility bundles) Repo: https://github.com/ClawBio/ClawBio Format: Python scripts with demos. Each analysis exports report.md + commands.sh + environment.yml.
How to fetch and use a skill
- Identify the domain and skill name from the index below.
- Clone the relevant repo (shallow clone to save time):
# bioSkills (reference material) git clone --depth 1 https://github.com/GPTomics/bioSkills.git ~/.hermes/cache/scratch/bioSkills # ClawBio (runnable pipelines) git clone --depth 1 https://github.com/ClawBio/ClawBio.git ~/.hermes/cache/scratch/ClawBio - Read the specific skill:
# bioSkills — each skill is at: <category>/<skill-name>/SKILL.md cat ~/.hermes/cache/scratch/bioSkills/variant-calling/gatk-variant-calling/SKILL.md # ClawBio — each skill is at: skills/<skill-name>/ cat ~/.hermes/cache/scratch/ClawBio/skills/pharmgx-reporter/README.md - Follow the fetched skill as reference material. These are NOT Hermes-format skills — treat them as expert domain guides. They contain correct parameters, proper tool flags, and validated pipelines.
Skill Index by Domain
Sequence Fundamentals
bioSkills: sequence-io/ — read-sequences, write-sequences, format-conversion, batch-processing, compressed-files, fastq-quality, filter-sequences, paired-end-fastq, sequence-statistics sequence-manipulation/ — seq-objects, reverse-complement, transcription-translation, motif-search, codon-usage, sequence-properties, sequence-slicing ClawBio: seq-wrangler — Sequence QC, alignment, and BAM processing (wraps FastQC, BWA, SAMtools)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago Changed 49cd910728b4
- 1mo ago First seen · 238 lines · 15 tokens per session scan B cebf83e4740b
bioinformatics is a skill published in the GitHub repository NousResearch/hermes-agent (256,529 stars, last pushed today), licensed MIT. It adds 15 tokens to every session and 3,388 once invoked, about $0.0001 per session on Opus 5.5. A static security scan graded it B with 1 finding (asks for root). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
function_health
Retrieve lab biomarker results and clinician notes from Function Health.
maps-geography
Accurate maps from real geo data — use for any map, or whenever geography would make a good graphic for a deliverable.
create-maps-and-spatial-plans
A guide for making maps and spatial plans based on real locations, boundaries, directions, scale, routes, floors, or access between places. It covers reference maps, navigation, thematic maps, service areas, site plans, and indoor wayfinding.
create-technical-diagrams
A guide for creating technical diagrams and engineering documents that show components, connections, processes, states, timing, interfaces, or cause and effect. It includes system and network diagrams, flow and sequence diagrams, electrical plans, mechanical sections, and scientific mechanism diagrams.
build-interactive-explainers
A guide for building interactive explainers, calculators, and simulations driven by an executable model. Users change inputs, steps, states, or events to understand a rule or see how a process develops over time.
biological-expert
Expert-level biology, biotechnology, genetics, bioinformatics, and computational biology. Use when the user mentions biology, biotechnology, genetics, bioinformatics, or genomics, or when the task involves Molecular Biology, Genomics & Bioinformatics, Systems Biology, or Data Analysis.